MICB425 Portfolio - Microbial Ecological Genomics: From Genomes to Biomes, Spring 2018
Student First Name, Preferred Name, Last Name, Student ID
version January 30, 2018
Module 01
Reserve the first level headings (#) for the start of a new Module. This will help to organize your portfolio in an intuitive fashion.
Note: Please edit this template to your heart’s content. This is meant to be the armature upon which you build your individual portfolio. You do not need to keep this instructive text in your final portfolio, although you do need to keep module and assignment names so we can identify what is what.
Module 01 portfolio check
The first of your second level headers (##) is to be used for the portfolio content checks. The Module 01 portfolio check has been built for you directly into this template, but will also be available as a stand-alone markdown document available on the MICB425 GitHub so that you know what is required in each module section in your portfolio. The completion status and comments will be filled in by the instructors during portfolio checks when your current portfolios are pulled from GitHub.
- Installation check
- Completion status:
- Comments:
- Portfolio repo setup
- Completion status:
- Comments:
- RMarkdown Pretty html Challenge
- Completion status:
- Comments:
- Evidence worksheet_01
- Completion status:
- Comments:
- Evidence worksheet_02
- Completion status:
- Comments:
- Evidence worksheet_03
- Completion status:
- Comments:
- Problem Set_01
- Completion status:
- Comments:
- Problem Set_02
- Completion status:
- Comments:
- Writing assessment_01
- Completion status:
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- Additional Readings
- Completion status:
- Comments
Data science Friday
The remaining second level headers (##) are for separating data science Friday, regular course, and project content. In this module, you will only need to include data science Friday and regular course content; projects will come later in the course.
Installation check
Third level headers (###) should be used for links to assignments, evidence worksheets, problem sets, and readings, as seen here.
Use this space to include your installation screenshots.
Portfolio repo setup
Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.
git add
and use git status to check
RMarkdown pretty html challenge
Paste your code from the in-class activity of recreating the example html.
version January 18, 2018
R Markdown PDF Challenge
The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.
http://phdcomics.com/ Comic posted 1-17-2018
Challenge Goals
The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
hint: go to the PhD Comics website to see if you can find the image above If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown
Here’s a header!
Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).
Another header, now with maths
Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:
1231521+12341556280987## [1] 1.234156e+13Table Time
Or maybe, after you’ve added those numbers, you feel like it’s about time for a table! I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in the future.
library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")| speed | dist | |
|---|---|---|
| Min. : 4.0 | Min. : 2.00 | |
| 1st Qu.:12.0 | 1st Qu.: 26.00 | |
| Median :15.0 | Median : 36.00 | |
| Mean :15.4 | Mean : 42.98 | |
| 3rd Qu.:19.0 | 3rd Qu.: 56.00 | |
| Max. :25.0 | Max. :120.00 |
And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun gif of your choice!
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Origins and Earth Systems
Evidence worksheet 01
The template for the first Evidence Worksheet has been included here. The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).
You can copy-paste in the answers you recorded when working through the evidence worksheet into this portfolio template.
As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t’ want to clutter the Table of Contents too much.
Learning objectives
Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
General questions
* What were the main questions being asked?
How do we estimate the prokaryotic population of the world? And what is it made up of?
What are the uncertainties that come with this measurement?
Which environments contain the most prokaryotic biomass?
How does this biomass affect global nutrient cycles? (e.g. P, C, N)
* What were the primary methodological approaches used?
Prokaryotic estimates were based upon average data from the following four environments: aquatic environments, soil, subsurface, and “other habitats” including in or on animal or plant surfaces or in the air. They used experimentally derived values to perform these calculations, but interestingly, not the same value sets for each environment. For example, some calculations included cell volume, while others included just the area of the environment. Vi
Also, they compared their calculated values with some from other papers, which resulted in some differences that they attempted to explain.
* Summarize the main results or findings.
They found that prokaryotes contain about half of the organic carbon on earth, and 90% of the nutrients (compared to plants) In brief, the prokaryotic biomass and thus their contribution to global cycles is very large - doubling estimates of the amount of carbon stored in living organisms globally. They broke down the calculations into four environments: aquatic environments, soil, subsurface, and “other habitats”.
Aquatic environments- this includes the open ocean, sediment in the ocean, freshwater and saline lakes (3 orders of magnitude less) and polar regions. Prokaryotes are ubiquitous in these environments - 1180 x 1026 cells.
Soil- surprisingly, there are less prokaryotes in forest soils than in other soils. The estimates varied by ecosystem. 255.6 x 1027 cells.
Subsurface- e.g. terrestrial habitats below 8 m and marine sediments below 10 cm. (this includes groundwater too) This environment is difficult to estimate because it is difficult to obtain uncontaminated samples. However, it has been suggested to be enormous. 3.8 x 1030 cells.
Other environments - discussed the prokaryotes that live on animals, insects, and plants, and also those in the air/atmosphere. 53.024 x 1023 cells (several orders of magnitude smaller)
These large numbers mean that not only carbon, but N and P are stored in globally significant amounts in prokaryotes.
Disproves Kluyver’s estimate that 1/2 of the living protoplasm on earth is microbial - likely this number is far too conservative. The paper also discusses growth rates to estimate cell turnover, and fluxes in and out of these environments.
* Do new questions arise from the results?
In subsurface environments, the turnover time of cells seems exceedingly large, is this a good estimate?
Where does the energy in the subsurface environments come from? Photosynthesis? Chemolithotrophy?
From the passage “in the polar regions, a relatively dense community of algae and prokaryotes forms at the water-ice interface” - why does this occur?
How accurate can these calculations be if they are based upon just a few estimates?
How much flux occurs among all of these prokaryotic environments? Especially the subsurface environment, if so many cells are hypothesized to be metabolically inactive, how much flux can occur? Is it more of a pool than a flux?
Problem set 01
Learning objectives:
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
Specific questions:
* What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.
The primary prokaryotic habitats on earth are split into aquatic habitats, soil, and subsurface habitats. According to table 5 of the text, there are 12 x 1028 cells in aquataic habitats, 26 x 1028 cells in the soil, and interestingly, 355 x 1028 and 25-250 x 1028 prokaryotic cells in the oceanic and terrestrial subsurface respectively. However, in order to rank these habitats based on their capacity to support life, we must come up with a universal definition for “capacity to support life”. If you were to define this as the total number of prokaryotic cells in a given habitat, it would appear that the oceanic subsurface habitat has the greatest capacity to support life. However, this does not take into account whether these cells are metabolically active, or their turnover time, or the total area occupied by the habitat.
* What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?
2.8 x 1028 cells in the upper 200m
The average density is 5 x 105 cells/mL
To calculate what fraction of this ratio are cyanobacteria:
4 x104 cells/ml / 5 x 105 cells/ml x 100 = 8%
This ratio is significant because these cells are autotrophs, which means that they are responsible for asimilating inorganic carbon into this environment, and thus are an important aspect of carbon cycling in the ocean. This is not only important for aquatic environments, but for the atmospheric composition of the earth as well. This is because some organic carbon fixed by these autotrophs are not respired and stored in marine sediment. Since respiring this material generally requires oxygen, its long-tem storage means that oxygen can remain in significant levels in the earth’s atmosphere. This is in contrast to terrestrial systems, where carbon fixed by autotrophs is generally respired.
* What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
Autotroph - produces organic complex carbons from simple inorganic substances such as carbon dioxide. Heterotroph - takes up organic carbon to produce energy and synthesize compounds Lithotroph - uses an inorganic substrate to obtain reducing equivalents for use in biosynthesis or energy conservation via aerobic or anaerobic respiration
* Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
Temperature is the limiting factor in subsurface environments, and at around 4 km in terestrial environments the temperature reaches 125 degrees celsius. This is the generally agreed upon temperature limit of prokaryotic life.
The deepest habitat capable of supporting prokaryotic life is the Mariana Trench, which is 10.9 km deep, then cellular life should be able to persist another 4 km deeper in the subsurface- so 14.9 km total.
* Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
Mount everest is 8.8 km high, so that would be the highest terestrial habitat capable of supporting prokaryotic life.
Additionally, in the text, bacteria in the air were discussed. However, are these bacteria actually metabolically active? They could just be spore formers, or metabolically inactive until they reach an environment that is more viable.
The paper stated 77 km, but this does not seem very realistic, because the limiting factors in these environments include nutrient availability, UV radiation, and temperature. So I would say more like 20 km high.
* Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
I would say that the vertical distance of the Earth’s biosphere is a range of 24 km - 34 km (due to the Mariana trench)
* How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
Population size x turnovers/year = cells/year
Marine heterotrophs: 3.6 x 1028 cells x 365 days / 16 days/turnover = 8.2 x 1029 cells/year
* What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
Assuming the carbon efficiency is 20% If there is around 5-20 fg of carbon in a prokaryotic cell, 20 fg C/cell = 20-30 Pg/cell
3.6 x 1028 cells x 20-30 Pg/cell = 0.72 Pg C are trapped in marine heterotrophs To calculate the total carbon flux, we should multiply this value by 5, but the authors used 4, so 4 x .72 = 2.88 Pg/year
51 Pg C/year, 85% of the carbon in the photic zone is consumed = 43 Pg C
43 Pg C/year / 2.88 Pg/year = 14.4 turnovers/year 1 turnover every 25.4 days
This varies with depth in the ocean due to access to sunlight, as photosynthesis provides the energy necessary for carbon fixation. In terestrial habitats, a number of factors including differences in depth, sediment, nutrient availability, and cell density contribute to the differences in carbon fixation and turnover rate.
* Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
Given the large population size and high mutation rate of prokaryotic cells, this indicates that prokaryotic cells have a very large adaptive potential. As prokaryotes have existed on the earth for billions of years, this corresponds to an incredibly large amount of genetic diversity.
However, it is foolhardy to assume that point mutations are the only way that microbial genomes diversify and adapt. Infection by bacteriophages can transport foreign DNA into a cell, some cells can share plasmids using conjugative pili, and others can uptake exogenous DNA from their environment. Additionally, other mutation events can occur independent of point mutations in a single cell, such as gene duplication or deletion.
* What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?
Based on the information provided in the text, I would say that prokaryotic abundance and metabolic potential is highly related to the diversity of organisms present in the biosphere. Given the large abundance of prokaryotic life, and its correspondingly large mutation rate, over the course of geologic time this has generated an incredibly diverse set of metabolic capabilities of individual prokaryotes. These different metabolic abilities have enabled prokaryotes to colonize the entire biosphere (24-34 km of the earth’s surface, subsurface, and lower atmosphere).
Evidence Worksheet_02 “Life and the Evolution of Earth’s Atmosphere”
Learning objectives:
Comment on the emergence of microbial life and the evolution of Earth systems
Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.
- 4.6 billion years ago
According to Nisbet et al, our solar system began after one or multiple supernova explosions. At this time, the inner planets (including earth) were formed from collisions between “planetesimals” - debris about the size of the earth’s moon.
+ 4.2 billion years ago The suggested origin of life (microbial) according to Nisbet et. al. Due to the intrinsically difficult nature of establishing an exact date, the origin of life is instead given in a range: 4.0+/-0.2 Gyr. This data is supported by the enrichment of “heavy” 13C in inorganic carbonate in rocks.
+ 3.8 billion years ago According to Nisbet et al, the earth suffered “frequent massive meteorite impacts”, some of which were large enough to cause the liquid water in the oceans to become steam.
+ 3.5 billion years ago Fossil evidence of microbial biofilms and stromatolites first appears. Additionally, increased isotopic evidence for life. This is when Rubisco, the enzyme necessary for oxygenic photosynthesis was thought to have developed. This is when LUCA - the Last Universal Common Ancestor of all life was thought to have lived.
+ 3.0 billion years agoSome evidence points to the emergence of the first continents as we know them today (albeit in different formations).
+ 2.7 billion years ago Initial rise of atmospheric O2, believed to be due to the rise of cyanobacteria. This is also when one of the first glaciation events occured, due to the decrease of CH4 in the atmosphere due to microbial processes.
+ 2.2 billion years ago There are some findings that hypothetically date life on land beginning as early as 2.2 billion years ago. However, microbial fossils are far from conclusive.
+ 2.1 billion years agoThe advent of the first complex (read, multicellular) organisms, or at least fossil evidence for them.
+ 1.3 billion years agoEvidence of the first land fungi: not photosynthetic land plants. Photosynthetic land plands were only thought to have evolved around 700 million years ago.
+ 550,000,000 years agoThe Cambrian explosion, when most modern day animal phyla are thought to have evolved. This was a major diversification of complex life on the planet.
+ 200,000 years agoThe first record of Homo Sapiens (us) in Africa.
Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:
- Hadean
The Hadean is generally established as 4.6 - 4 Gyr, and is contains the origin of earth as a planet to the origin of life on earth. During this time, meteorite bombardment levels were very high, and conditions on the surface were not well suited to life today. Nisbet et. al compares the Hadean earth to a “Norse Ice-Hades” with glacial temperatures interspersed with very high temperatures as a result of meteorite impacts. The oceans formed during this time period. Additionally, the early sun was fainter.
+ Archean Life developed during the Archaean (4-2.5 Gyr). Volcanic activity was very high, and due to the advent of oxygenic photosynthesis, the beginning of the oxygenation of the earth’s atmosphere occured.
+ Precambrian The Precambrian Supereon stretches from 4.6 Gyr - 0.56 Gyr, and contains the Hadean, Archean, and Proterozoic (but not the Phanerozoic) eons. The Earth went through a wide variety of physical and chemical characteristics during this time (see other sections for details).
+ Proterozoic 2.5-0.56 Gyr. Oxygenation of the earth’s atmosphere continued, finally reaching significant levels due to the proliferation of oxygenic photosynthesis. This established conditions necesary for the first complex and multicellular organisms. As the sun’s luminosity increases by 6% every billion years, the earth begins to recieve more heat from the sun. However, there is evidence that the earth cooled during this period, a hypothesis known as Snowball Earth due to changes in the cheical composition of the atmosphere.
+ Phanerozoic 0.56 Gyr to present day. This eon encompasses the development of land plants and land life, as well as the origins of most of the recognized animal phyla to this day. This comparatively small (considering the extent of the precambrian superepoch) epoch also contains several planetary extinction events establishment of land masses as we know them today.
Module 01 references
Utilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.
An example for Whitman and Wiebe (1998) has been included below.
Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863
Kasting JF,and Siefert JL. 2003. Life and the Evolution of Earth’s Atmosphere. Science. 296: 1066-1067. (https://www.ncbi.nlm.nih.gov/pubmed?term=Science%5BJour%5D+AND+Life+and+the+Evolution+of+Earth’s+Atmosphere&TransSchema=title&cmd=detailssearch)
Nisbet EG, and Sleep NH. 2001. The habitat and nature of early life. Nature. 409: 1083-1091.
Orndoroff RC, et al. 2007. Divisions of Geologic Time - Major Chronostratigraphic and Geochronologic Units. Fact Sheet 2007-3015. U.S. Department of the Interior and U.S. Geological Survey.